Genomic characterization of the Pantoea allii strain for biotechnological applications

Members of the genus Pantoea are known for their high ecological plasticity and diverse interactions with plants, ranging from phytopathogenic to commensal, symbiotic, and growth-promoting. Some of its strains have significant biotechnological potential due to their ability to synthesize phytohormones, siderophores, and antimicrobial secondary metabolites. In this study, we aimed to conduct whole-genome sequencing of the strain Pantoea allii B-14727 to identify genetic determinants associated with its antagonistic activity, competitiveness, and colonizing capacity. The strain under study was initially identified as Pantoea vagans B-14727 by the 16S rRNA gene and deposited at the All-Russian Collection of Industrial Microorganisms at the Kurchatov Institute National Bioresource Center (Russia). However, based on whole-genome sequencing, its species identity was revised as P. allii. Its DNA was extracted with a ZymoBIOMICS DNA Miniprep Kit. Genomic sequencing was performed on the MGIseq-2000 and Polyseq One platforms, with libraries prepared by using standard NEBNext and Barcode/Ligation kits. The strain’s genome was annotated using Bakta software, and its taxonomic identification was performed using GTDB-Tk and the GTDB database. The P. allii B-14727 genome contained NRPS-independent siderophores (aerobactin and desferrioxamine E), terpene carotenoid clusters, RiPP peptides, and a hybrid PKS/NRPS cluster similar to the biosynthetic pathway of zeamine and its derivatives. Siderophores ensure efficient iron uptake, making the strain more competitive in conditions of iron deficiency. Carotenoids exhibit antioxidant and photoprotective functions, increasing cellular resistance to abiotic stress. The hybrid zeamine cluster contributes to the synthesis of broad-spectrum peptide antibiotics with antibacterial and fungicidal activity. The biosynthetic systems identified in P. allii B-14727 indicate its pronounced adaptive and competitive potential. However, the strain’s non-virulent status needs to be confirmed prior to further practical applications.